The Regeneration
by SonarTheHedgehog
Summary: The Doctor regenerates into his 12th incarnation...but now things have changed drastically. The Doctor is not only far different, but it turns out that even more powerful forces have affected not only the regeneration process, but are also trying to revive Gallifrey, and create a new universal empire, but this is not without consequences...The Doctor will see you now.
1. Chapter 1

The Doctor lay on the floor, gasping, listening to the sounds of the TARDIS as she hummed and flew through time and space. He had just let Amy and Rory off back on Earth; they had wanted some alone time for a few months. And as the Doctor had been walking back to the TARDIS in the streets, a simple mugger had attacked him. The Doctor who could fight off Daleks, weeping angels, and all sorts of other insanely powerful creatures, yet it was a simple, weak human who had hurt him.

And unfortunately, these wounds were killing him. The Doctor had managed to drag himself back to the TARDIS, where "she" had automatically opened the door for him, probably somehow sensing his pain. The inevitable was coming; the Doctor would have to regenerate, and turn into his twelfth incarnation.

He chuckled to himself as the TARDIS continued to hum, carrying him away to nowhere in particular; maybe he would turn into a ginger. Another part of him was sad though; he liked eating fish fingers with custard, saying "Geronimo", wearing bowties and the occasional fez… Even though he would remember these things, and having liked them, didn't mean that they would necessarily remain the same. But hey, he could still potentially still like all of those things after regenerating. After all, both his ninth and tenth incarnations had liked bananas. Certainly the Doctor would still like some of the same things in his twelfth incarnation!

A searing, burning hot sensation shot through his body; the reincarnation process had officially begun. It was too late. The faint glowing had started, and at the peak of the cycle, it would erupt into light all around him. The Doctor dragged himself over to the control console, and pulled a lever. He wanted to land on a planet and get outside of the TARDIS before that part of the process occurred, otherwise the TARDIS would experience quite a deal of damage as she had done when he had last transformed.

The TARDIS landed on some uninhabited planet, but that didn't really matter to the Doctor at that moment. He just had to get outside. Obligingly, the TARDIS opened the door for him as he staggered to his feet, blood staining his shirt. He patted the doorframe as he stumbled out.

"I won't be long, you sexy thing. I just can't have you getting wrecked again like last time, eh?"

The Doctor managed to stagger about another twenty yards before he finally collapsed to the ground. The light was growing brighter, and the moment had finally come. He shut his eyes as the light, as HE exploded, his body morphing and twisting into a new individual. In his minds eye, he thought of all the companions he'd ever had, and if Rory and Amy would still travel with him, if River would still love him in a new form.

Finally, the pain stopped, and the heat faded away. The Doctor sat up, curly gold locks of hair cascading down his back. He inspected his hands; they were smaller and daintier. And for some reason his clothes were much larger on him than before, and there were lumps under the shirt. The Doctor stood to walk to the TARDIS, when his shoes fell straight off; they were too big. The Doctor began to fear what all of this meant, and ran into the TARDIS on the border of hysteria.

The Doctor grabbed a mirror, and stared into it. The eyes were definitely still the same, and the prominent cheekbones were still there, but the lips were red, and the eyelashes were long and thick, and he was most definitely a GIRL. He was now a she.

The Doctor screamed. Far away, Amy Pond felt a shiver run down her back.


	2. Chapter 2

The TARDIS could sense the Doctor's obvious distress, and shut the doors, and automatically took off for the time vortex. The Doctor could only stand in front of the bathroom mirror, tugging at the ridiculously long, NOT GINGER curls in disbelief. This was a rare occurrence, for a time lord to change gender. The Doctor had barely believed in such a thing.

She walked back into the console room, clothes hanging off of her tiny frame in a comical sort of way, sighing as she went.

The Doctor didn't really care where the TARDIS was going right then. Humming around the vortex was just fine by her at the moment.

"What am I going to do, Sexy?" The Doctor asked the TARDIS, frustrated. The TARDIS made a noise that sounded like an amused, but comforting laugh. The hallway leading to the kitchen lit up briefly; the TARDIS was telling the Doctor to go figure out what she liked now. And the Doctor had that weird apple craving again…

Apples were absolute rubbish. Wine was still as nasty as ever, beans were bad, bread and butter were okay, but fish fingers and custard were still as heavenly as ever. If there was anything the Doctor could count on, it was fish fingers and custard.

The Doctor walked back out of the kitchen, still dressed in her old clothes. The sleeves were rolled up, but it didn't help much except to let her function.

She walked into the TARDIS wardrobe, trying to see if she could find something to wear, and unable to find anything. The TARDIS was aimed at the tastes of River and Amy, not her.

"Sexy, I'm going to take a bath. I'm trusting you to pick out my clothes this time," the Doctor said.

By the time the Doctor reached the nearest bathroom, the water was already running, and towels and hair products were lying out, ready for use. The TARDIS was clearly trying to make the transition as easy as possible, and the Doctor couldn't feel more grateful.

"Thank you, Sexy," the Doctor murmured as she pulled off the bloodstained clothing, flinging it to the floor. She sank into the bath water, the heat loosening the tension and stress inside. The time lord simply lay in the tub for a while, steam rising above the bubbly water, water soaking into her long hair.

After a while, she washed and conditioned her hair, listening to the relative silence of the TARDIS. All the Doctor could hear was the faint humming of the TARDIS as she glided through the time vortex, the plips of water, and her own twin heartbeats. But the silence was good. Just for a little bit.

After rinsing herself and her hair out, the Doctor finally pulled herself out of the tub, wrapping a towel around her body as she did. She was suddenly exhausted beyond belief, and forgot about seeing what the TARDIS had decided to clothe her in. The Doctor stumbled into her room, filled with pictures of companions and past incarnations, and other trinkets from all of the adventures. She fell onto the bed wearing only a towel, and fell asleep, not caring about anything at all.

The Doctor woke up sometime later, disoriented and confused. Her hair had dried, long and curly as when she had just regenerated. She sat up groggily, trying to think.

_I'm the Doctor. I'm from Gallifrey, which is gone. The universe thinks I'm dead, except for three people. And now I'm a woman. Oh yeah. OH NO._

She looked down, suddenly remembering the regeneration, all grogginess leaving her. The Doctor sighed, and pulled the towel up around to cover her, and walked out into the hallway, heading again for the bathroom.

After combing her hair out, the Doctor went back to the wardrobe to find clothes. The TARDIS hadn't let her down, that was certain. Sexy had left her with a blue dress and short-sleeved overcoat, stockings, and red pumps. Apparently the TARDIS liked the whole "Alice" look, but really, the Doctor wasn't going to complain, and was fine with it.

As the Doctor finished putting it all on, the TARDIS suddenly chucked a hair ribbon at her at a rather high velocity, as if it was an afterthought. So, the Doctor went back to the bathroom to put it in her hair, grinning a little as she heard the TARDIS wheeze in approval.

She bounced back out into the console room, inspecting their course. It was set for Earth, year 1776. But the Doctor had never set a course…

She then remembered when she had the conversation with the TARDIS, had said. _"I may not have always taken you where you wanted to go, but I've always taken you where you NEEDED to go."_ And for the Doctor, that was enough.

"Okay old girl, take me where I'm needed," the Doctor urged as she pulled some levers. The TARDIS began to accelerate, almost causing the Doctor to drop the psychic paper and sonic screwdriver as she pocketed them into her apron.

The Doctor pressed another button, sending the TARDIS to the peak of acceleration as it hurtled across time and exited the vortex, approaching Earth. The speed was exhilarating, and the Doctor needed the rush.

"Geronimo!"

The one thing the Doctor knew was important about this year as she stepped out of the TARDIS onto the streets of London was that this was the year that America proclaimed independence, leaving the English government devastated and furious. She scanned the streets, searching for something out of place, anything.

The Doctor cloaked the TARDIS to keep it from prying eyes, and then began to search around, walking along the cobble stone streets, casually inspecting the carriages and the people for anyone unusual.

But as she continued to wander and saw nothing, another individual watched her from afar, and rose from his lookout on a rooftop. Within a minute, he was back inside the building, and out onto the street again.

Nothing was going to keep the Master from carrying out his plans this time. Absolutely nothing.


	3. Chapter 3

The Doctor really couldn't help but sigh a little. She couldn't find a single thing out of place here. No alien invasions, no weird machines, absolutely nothing. It really was just 1776 London.

She walked along the cobbled streets, avoiding the rubbish tossed from windows above. The Doctor turned a corner, only to end up on a much quieter and narrower street. She was considering turning back to go to the TARDIS, when she suddenly felt a strong psychic presence from behind her. The presence of a time lord, of all things. The Doctor whirled around, only to find the Master, clad in a well-tailored suit, face shaven, hair as bleach-blond as when she had last seen him.

"Hello, Doctor. Miss me?"

"You e-escaped the t-time lock," the Doctor could only stammer back. "How? What happened?"

"Walk with me and I'll tell you."

-Dooooo Weeeeeee Ooooooooo-

"So, let me get this straight," the Doctor said. "The time lock broke, and you along with some other time lords managed to escape before Gallifrey exploded. And now Rassilon is looking for a new Gallifrey so he can rebuild the time lord race, and, as you claim, eventually take control over the known universe."

"Yeah, pretty much," the Master replied coolly.

The two children of Gallifrey sat in a small restaurant across from each other, feeling rather awkward. Well, the Doctor felt awkward. The Master seemed to be enjoying himself.

"I don't mind the time lords returning to the face of the universe," the Master said. "But you should have heard Rassilon. He's insane. He's teamed up with the Silence, and-"

"Oh, no. They think I'm dead, currently," the Doctor said. "Madame Kovarian hasn't bothered me since-"

"Oh, trust me Doctor, I know all about what you've been doing. Pretty clever to use the Tesselecta. It also helps that you're female right now. Kovarian and her Silence think you're a man, and a dead one at that."

"So," the Doctor said, sitting forward in her chair a bit. "Why did you come looking for me?"

The Master leaned forward as well. "Help me stop Rassilon. All those years ago you ran away from the corruption of the time lords, and maybe we can fix it."

The Doctor cocked an eyebrow. "You're outlook on life and the universe has certainly changed."

"It helps that the drums are gone. I feel like I can actually think clearly for once."

"But why me? You and I have always been at odds," the Doctor replied, rising from her chair. The Master rose as well, and they headed out into the sun together.

"Doctor," the Master said. "Really, what would I be without you?"

This made the Doctor stop, looking back at all of their encounters, the time when they were young, running through fields of red grass. All the times when the Master was trying to kill. When the Master had saved her tenth incarnation, and sealing himself into the time lock.

"All right," the Doctor said. "Where do we start?"

-Fezzes-

"How did you get a TARDIS?"

"I stole it," the Master replied, looking rather pleased with himself. "It's Rassilon's TARDIS. He had to ride in someone else's."

The Doctor turned to look at him slowly, face completely white as she stared at the time machine in front of her. "Rassilon's TARDIS. RASSILON."

"Yes."

"He is going to murder you, and brutally. Really, Koschei?"

The Master laughed a bit. "Go and get your TARDIS, then land it inside of mine. Makes it easier to travel instead of meeting up everywhere."

The Doctor decided to comply, and walked back to her Sexy TARDIS, shaking her head. The Master was going to get himself killed. She was a madwoman with a box, but at least she didn't function at the Master's level of crazy. Or rather, what used to be his level of crazy.

Inside his stolen TARDIS, the Master sat waiting for the Doctor, watching Teletubbies.


End file.
